Annotation inject logs

.github/workflows/protect-master.yml

@@ -25,6 +25,6 @@ jobs:
 
       # Test using proper JDK and MVN
       - name: Test
-        uses: docker://maven:3-eclipse-temurin-21
+        uses: docker://maven:3-eclipse-temurin-17
         with:
           args: mvn test

s-pipes-cli/pom.xml

@@ -53,6 +53,11 @@
             <artifactId>logback-core</artifactId>
             <version>${ch.qos.logback.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <scope>provided</scope>
+        </dependency>
         <!-- IO utils -->
         <dependency>
             <groupId>commons-io</groupId>
@@ -72,6 +77,8 @@
         </dependency>
     </dependencies>
 
+
+
     <build>
         <plugins>
             <plugin>

s-pipes-cli/src/main/java/cz/cvut/spipes/cli/ExecuteModuleCLI.java

@@ -7,6 +7,7 @@
 import cz.cvut.spipes.manager.OntologyDocumentManager;
 import cz.cvut.spipes.manager.SPipesScriptManager;
 import cz.cvut.spipes.modules.Module;
+import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.QuerySolutionMap;
 import org.apache.jena.rdf.model.Model;
@@ -29,7 +30,7 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-
+@Slf4j
 public class ExecuteModuleCLI {
 
     // cat input-data.rdf | s-pipes execute --instance "<http://url>"
@@ -39,7 +40,7 @@ public class ExecuteModuleCLI {
     // > output.data.rdf
 
 
-    private static final Logger LOG = LoggerFactory.getLogger(ExecuteModuleCLI.class);
+
     private static final String DEFAULT_DELIMITER = ";";
     //@Option(name = "-d", aliases = "--delimiter", metaVar = "DELIMITER", usage = "Input variables data delimiter ('" + DEFAULT_DELIMITER + "' by default)")
     //private String delimiter = DEFAULT_DELIMITER;
@@ -98,32 +99,32 @@ public static void main(String[] args) throws IOException {
         CmdLineUtils.parseCommandLine(args, argParser);
 
         String output = String.join(" ", args);
-        LOG.info("Executing external module/function ... " + output);
+        log.info("Executing external module/function ... " + output);
 
         // ----- load input model
         Model inputDataModel = ModelFactory.createDefaultModel();
 
         if (asArgs.inputDataFiles != null) {
             for (File idFile : asArgs.inputDataFiles) {
-                LOG.debug("Loading input data from file {} ...", idFile);
+                log.debug("Loading input data from file {} ...", idFile);
                 inputDataModel.read(new FileInputStream(idFile), null, FileUtils.langTurtle);
             }
         }
         if (asArgs.isInputDataFromStdIn) {
-            LOG.info("Loading input data from std-in ...");
+            log.info("Loading input data from std-in ...");
             inputDataModel.read(System.in, null, FileUtils.langTurtle);
         }
 
         // ----- load modules and functions
-        LOG.debug("Loading  scripts ...");
+        log.debug("Loading  scripts ...");
         SPipesScriptManager scriptManager = scriptManager = createSPipesScriptManager();
         OntoDocManager.registerAllSPINModules();
 
         // ----- load input bindings
         VariablesBinding inputVariablesBinding = new VariablesBinding();
         if (asArgs.inputBindingParametersMap != null) {
             inputVariablesBinding = new VariablesBinding(transform(asArgs.inputBindingParametersMap));
-            LOG.info("Loaded input variable binding ={}", inputVariablesBinding);
+            log.info("Loaded input variable binding ={}", inputVariablesBinding);
         }
 
         // ----- create execution context
@@ -139,7 +140,7 @@ public static void main(String[] args) throws IOException {
         }
         ExecutionContext outputExecutionContext = engine.executePipeline(module, inputExecutionContext);
 
-        LOG.info("Processing successfully finished.");
+        log.info("Processing successfully finished.");
        // outputExecutionContext.getDefaultModel().write(System.out);
 
 //        Model inputBindingModel = null;
@@ -265,7 +266,7 @@ private static SPipesScriptManager createSPipesScriptManager() {
 
         // load from environment variables
         String spipesOntologiesPathsStr = System.getenv(AppConstants.SYSVAR_SPIPES_ONTOLOGIES_PATH);
-        LOG.debug("Loading scripts from system variable {} = {}", AppConstants.SYSVAR_SPIPES_ONTOLOGIES_PATH, spipesOntologiesPathsStr);
+        log.debug("Loading scripts from system variable {} = {}", AppConstants.SYSVAR_SPIPES_ONTOLOGIES_PATH, spipesOntologiesPathsStr);
         if (spipesOntologiesPathsStr != null) {
             scriptPaths.addAll(
                     Arrays.stream(spipesOntologiesPathsStr.split(";"))
@@ -303,7 +304,7 @@ public static List<String> registerGlobalScripts(OntologyDocumentManager ontDocM
                 ontoUri -> {
                     String loc = locMapper.getAltEntry(ontoUri);
                     if (loc.endsWith(".sms.ttl")) {
-                        LOG.info("Registering script from file " + loc + ".");
+                        log.info("Registering script from file " + loc + ".");
                         _globalScripts.add(ontoUri);
                     }
                 }

s-pipes-core/pom.xml

@@ -44,6 +44,12 @@
             <artifactId>logback-classic</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <scope>provided</scope>
+        </dependency>
+
         <!-- Test dependencies -->
         <dependency>
             <groupId>org.junit.jupiter</groupId>

s-pipes-core/src/main/java/cz/cvut/spipes/engine/ExecutionEngineImpl.java

@@ -1,6 +1,7 @@
 package cz.cvut.spipes.engine;
 
 import cz.cvut.spipes.modules.Module;
+import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -14,16 +15,16 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+@Slf4j
 class ExecutionEngineImpl implements ExecutionEngine {
 
-    private static Logger LOG = LoggerFactory.getLogger(ExecutionEngineImpl.class);
 
     private Set<ProgressListener> listeners = new HashSet<>();
 
     private static int i = 0 ;
 
     public ExecutionContext executePipeline(final Module module, final ExecutionContext inputContext) {
-        LOG.info("Executing script {} with context {}.", module.getResource(), inputContext.toSimpleString());
+        log.info("Executing script {} with context {}.", module.getResource(), inputContext.toSimpleString());
         final long pipelineExecutionId = Instant.now().toEpochMilli()*1000+(i++);
 
         fire((l) -> {l.pipelineExecutionStarted(pipelineExecutionId); return null;});
@@ -37,7 +38,7 @@ private void fire(final Function<ProgressListener,Void> function) {
             try {
                 function.apply(listener);
             } catch(final Exception e) {
-                LOG.warn("Listener {} failed.", listener, e);
+                log.warn("Listener {} failed.", listener, e);
             }
         });
     }
@@ -58,17 +59,17 @@ private ExecutionContext _executePipeline(long pipelineExecutionId, Module modul
             fire((l) -> {l.moduleExecutionStarted(pipelineExecutionId, moduleExecutionId, module, context, predecessorId); return null;});
 
             if (module.getExecutionContext() != null) {
-                LOG.debug("Execution context for module {} already set.", module);
+                log.debug("Execution context for module {} already set.", module);
             } else {
                 module.setInputContext(context);
 
-                LOG.info(" ##### " + module.getLabel());
-                if (LOG.isTraceEnabled()) {
-                    LOG.trace("Using input context {}", context.toTruncatedSimpleString()); //TODO redundant code -> merge
+                log.info(" ##### " + module.getLabel());
+                if (log.isTraceEnabled()) {
+                    log.trace("Using input context {}", context.toTruncatedSimpleString()); //TODO redundant code -> merge
                 }
                 ExecutionContext outputContext = module.execute();
-                if (LOG.isTraceEnabled()) {
-                    LOG.trace("Returning output context {}", outputContext.toSimpleString());
+                if (log.isTraceEnabled()) {
+                    log.trace("Returning output context {}", outputContext.toSimpleString());
                 }
                 module.addOutputBindings(context.getVariablesBinding());
             }
@@ -80,18 +81,18 @@ private ExecutionContext _executePipeline(long pipelineExecutionId, Module modul
                 .collect(Collectors.toMap(Module::getResource, mod -> this._executePipeline(pipelineExecutionId, mod, context, moduleExecutionId)));
 
 
-        LOG.info(" ##### " + module.getLabel());
+        log.info(" ##### " + module.getLabel());
         ExecutionContext mergedContext = mergeContexts(resource2ContextMap);
-        if (LOG.isTraceEnabled()) {
-            LOG.trace("Using input merged context {}", mergedContext.toTruncatedSimpleString());
+        if (log.isTraceEnabled()) {
+            log.trace("Using input merged context {}", mergedContext.toTruncatedSimpleString());
         }
         fire((l) -> {l.moduleExecutionStarted(pipelineExecutionId, moduleExecutionId, module, mergedContext, predecessorId); return null;});
 
         module.setInputContext(mergedContext);
 
         ExecutionContext outputContext = module.execute();
-        if (LOG.isTraceEnabled()) {
-            LOG.trace("Returning output context {}", outputContext.toSimpleString());
+        if (log.isTraceEnabled()) {
+            log.trace("Returning output context {}", outputContext.toSimpleString());
         }
         module.addOutputBindings(mergedContext.getVariablesBinding());
         fire((l) -> {l.moduleExecutionFinished(pipelineExecutionId, moduleExecutionId, module); return null;});
@@ -128,7 +129,7 @@ private ExecutionContext mergeContexts(Map<Resource, ExecutionContext> resource2
             VariablesBinding conflictingBinding = variablesBinding.extendConsistently(b);
 
             if (! conflictingBinding.isEmpty()) {
-                LOG.warn("Module {} has conflicting variables binding {} with sibling modules ocurring in pipeline. ", modRes, context);
+                log.warn("Module {} has conflicting variables binding {} with sibling modules ocurring in pipeline. ", modRes, context);
             }
         });
 

s-pipes-core/src/main/java/cz/cvut/spipes/engine/PipelineFactory.java

@@ -13,6 +13,8 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
+
+import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -28,10 +30,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Slf4j
 public class PipelineFactory {
 
-    private static final Logger LOG = LoggerFactory.getLogger(PipelineFactory.class);
-
     // TODO inheritence not involved, not static context
     static Map<Resource, Class<? extends Module>> moduleTypes = new HashMap<>();
 
@@ -54,12 +55,12 @@ public static void registerModuleType(Resource moduleType, Class<? extends Modul
     }
 
     private static void _registerModuleType(Resource moduleType, Class<? extends Module> moduleClass) {
-        LOG.info(" module: {} -> {}", moduleType, moduleClass);
+        log.info(" module: {} -> {}", moduleType, moduleClass);
         moduleTypes.put(moduleType, moduleClass);
     }
 
     private static void _registerFunctionType(Resource functionType, Class<? extends ARQFunction> functionClass) {
-        LOG.info(" function: {} -> {}", functionType, functionClass);
+        log.info(" function: {} -> {}", functionType, functionClass);
         FunctionRegistry.get().put(functionType.getURI(), functionClass);
     }
 
@@ -114,7 +115,7 @@ public static Module loadModule(@NotNull Resource moduleRes) {
         // TODO multiple module types per resource
         Resource moduleTypeRes = moduleRes.getPropertyResourceValue(RDF.type);
         if (moduleTypeRes == null) {
-            LOG.error("Cannot load module {} as its {} property value is missing.", moduleRes, RDF.type);
+            log.error("Cannot load module {} as its {} property value is missing.", moduleRes, RDF.type);
             return null;
         }
         return loadModule(moduleRes, moduleTypeRes);
@@ -173,7 +174,7 @@ private static Map<Resource, Module> loadAllModules(@NotNull Model configModel)
                             .map(st -> {
                                 Module m = res2ModuleMap.get(st.getObject().asResource());
                                 if (m == null) {
-                                    LOG.error("Ignoring statement {}. The object of the triple must have rdf:type {}.", st, SM.Module);
+                                    log.error("Ignoring statement {}. The object of the triple must have rdf:type {}.", st, SM.Module);
                                 }
                                 return m;
                             }).filter(m -> (m != null)).forEach(
@@ -193,7 +194,7 @@ private static Module loadModule(@NotNull Resource moduleRes, @NotNull Resource
         Class<? extends Module> moduleClass = moduleTypes.get(moduleTypeRes);
 
         if (moduleClass == null) {
-            LOG.error("Ignoring module {}. Its type {} is not registered.", moduleRes, moduleTypeRes);
+            log.error("Ignoring module {}. Its type {} is not registered.", moduleRes, moduleTypeRes);
             return null;
         }
 

s-pipes-core/src/main/java/cz/cvut/spipes/engine/VariablesBinding.java

@@ -1,5 +1,6 @@
 package cz.cvut.spipes.engine;
 
+import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.QuerySolutionMap;
 import org.apache.jena.rdf.model.*;
@@ -14,11 +15,10 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+@Slf4j
 public class VariablesBinding {
 
     // TODO stream variables etc.
-
-    private static Logger LOG = LoggerFactory.getLogger(VariablesBinding.class);
     private static final int MAX_TRUNCATED_VALUE_SIZE = 300;
     QuerySolutionMap binding = new QuerySolutionMap();
 
@@ -31,7 +31,7 @@ public VariablesBinding(QuerySolution querySolution) {
                 key -> {
                     RDFNode value = querySolution.get(key);
                     if (value == null) {
-                        LOG.error("Ignoring variable binding with null value for the variable name \"{}\".", key);
+                        log.error("Ignoring variable binding with null value for the variable name \"{}\".", key);
                     } else {
                         binding.add(key, value);
                     }
@@ -79,7 +79,7 @@ public VariablesBinding extendConsistently(VariablesBinding newVarsBinding) {
 
                     if ((oldNode != null) && (!oldNode.equals(newNode))) {
                         conflictingBinding.add(v, newNode);
-                        LOG.warn("Variable \"{}\" have been bind to value \"{}\", ignoring assignment to value \"{}\".", v, oldNode, newNode);
+                        log.warn("Variable \"{}\" have been bind to value \"{}\", ignoring assignment to value \"{}\".", v, oldNode, newNode);
                     } else {
                         this.add(v, newNode);
                     }

s-pipes-core/src/main/java/cz/cvut/spipes/logging/AdvancedLoggingProgressListener.java

@@ -15,6 +15,7 @@
 import cz.cvut.spipes.util.DateUtils;
 import cz.cvut.spipes.util.Rdf4jUtils;
 import cz.cvut.spipes.util.TempFileUtils;
+import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.Property;
 import org.apache.jena.rdf.model.Resource;
@@ -45,9 +46,8 @@
 import java.nio.file.Paths;
 import java.util.*;
 
+@Slf4j
 public class AdvancedLoggingProgressListener implements ProgressListener {
-    private static final Logger LOG =
-        LoggerFactory.getLogger(AdvancedLoggingProgressListener.class);
     /**
      * Maps pipeline executions and module executions to the transformation object.
      */
@@ -173,7 +173,7 @@ private void persistPipelineExecutionFinished2(final EntityManager em, final lon
 
     private void persistPipelineExecutionFinished(final EntityManager em, final long pipelineExecutionId) {
         if (em.isOpen()) {
-            LOG.debug("Saving metadata about finished pipeline execution {}.", pipelineExecutionId);
+            log.debug("Saving metadata about finished pipeline execution {}.", pipelineExecutionId);
             Date finishDate = new Date();
             em.getTransaction().begin();
 
@@ -359,7 +359,7 @@ private void writeRawData(EntityManager em, URI contextUri, Model model) {
                 connection.getValueFactory().createIRI(contextUri.toString()));
             connection.commit();
         } catch (final RepositoryException | RDFParseException | RepositoryConfigException | IOException e) {
-            LOG.error(e.getMessage(), e);
+            log.error(e.getMessage(), e);
         } finally {
             if (connection != null && connection.isOpen()) {
                 connection.close();
@@ -386,7 +386,7 @@ private void saveModelToFile(String filePath, Model model) {
         try (OutputStream fileIs = new FileOutputStream(file)) {
             model.write(fileIs, FileUtils.langTurtle);
         } catch (IOException e) {
-            LOG.error("Error during dataset snapshot saving.", e);
+            log.error("Error during dataset snapshot saving.", e);
         }
     }